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rdd
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read
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recalibration
RecalibrationTable
class
RecalibrationTable
extends (
DecadentRead
) ⇒
Seq
[
QualityScore
] with
Serializable
Linear Supertypes
Serializable
,
Serializable
, (
DecadentRead
) ⇒
Seq
[
QualityScore
],
AnyRef
,
Any
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Inherited
RecalibrationTable
Serializable
Serializable
Function1
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Any
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Public
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Instance Constructors
new
RecalibrationTable
(
covariates:
CovariateSpace
,
globalTable:
Map
[
String
, (
Aggregate
,
QualityTable
)]
)
Value Members
final
def
!=
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
!=
(
arg0:
Any
)
:
Boolean
Definition Classes
Any
final
def
##
()
:
Int
Definition Classes
AnyRef → Any
final
def
==
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
==
(
arg0:
Any
)
:
Boolean
Definition Classes
Any
def
andThen
[
A
]
(
g: (
Seq
[
QualityScore
]) ⇒
A
)
: (
DecadentRead
) ⇒
A
Definition Classes
Function1
Annotations
@unspecialized
()
def
apply
(
read:
DecadentRead
)
:
Seq
[
QualityScore
]
Definition Classes
RecalibrationTable
→ Function1
final
def
asInstanceOf
[
T0
]
:
T0
Definition Classes
Any
def
clone
()
:
AnyRef
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
...
)
def
compose
[
A
]
(
g: (
A
) ⇒
DecadentRead
)
: (
A
) ⇒
Seq
[
QualityScore
]
Definition Classes
Function1
Annotations
@unspecialized
()
def
computeExtrasDelta
(
maybeQualityEntry:
Option
[(
Aggregate
,
ExtrasTables
)]
,
residueIndex:
Int
,
extraValues:
IndexedSeq
[
Seq
[
Option
[
Value
]]]
,
offset:
Double
)
:
Double
def
computeGlobalDelta
(
globalEntry:
Option
[(
Aggregate
,
QualityTable
)]
)
:
Double
def
computeQualityDelta
(
qualityEntry:
Option
[(
Aggregate
,
ExtrasTables
)]
,
offset:
Double
)
:
Double
val
covariates
:
CovariateSpace
final
def
eq
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
def
equals
(
arg0:
Any
)
:
Boolean
Definition Classes
AnyRef → Any
def
finalize
()
:
Unit
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
classOf[java.lang.Throwable]
)
final
def
getClass
()
:
Class
[_]
Definition Classes
AnyRef → Any
def
getExtraValues
(
read:
DecadentRead
)
:
IndexedSeq
[
Seq
[
Option
[
Value
]]]
def
getQualityEntry
(
quality:
QualityScore
,
globalEntry:
Option
[(
Aggregate
,
QualityTable
)]
)
:
Option
[(
Aggregate
,
ExtrasTables
)]
val
globalTable
:
Map
[
String
, (
Aggregate
,
QualityTable
)]
def
hashCode
()
:
Int
Definition Classes
AnyRef → Any
final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
def
lookup
(
residueWithIndex: (
Residue
,
Int
)
,
globalEntry:
Option
[(
Aggregate
,
QualityTable
)]
,
globalDelta:
Double
,
extraValues:
IndexedSeq
[
Seq
[
Option
[
Value
]]]
)
:
QualityScore
val
maxLogP
:
Double
val
maxQualScore
:
QualityScore
final
def
ne
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
notify
()
:
Unit
Definition Classes
AnyRef
final
def
notifyAll
()
:
Unit
Definition Classes
AnyRef
def
qualityFromLogP
(
logP:
Double
)
:
QualityScore
final
def
synchronized
[
T0
]
(
arg0: ⇒
T0
)
:
T0
Definition Classes
AnyRef
def
toString
()
:
String
Definition Classes
Function1 → AnyRef → Any
final
def
wait
()
:
Unit
Definition Classes
AnyRef
Annotations
@throws
(
...
)
final
def
wait
(
arg0:
Long
,
arg1:
Int
)
:
Unit
Definition Classes
AnyRef
Annotations
@throws
(
...
)
final
def
wait
(
arg0:
Long
)
:
Unit
Definition Classes
AnyRef
Annotations
@throws
(
...
)
Inherited from
Serializable
Inherited from
Serializable
Inherited from (
DecadentRead
) ⇒
Seq
[
QualityScore
]
Inherited from
AnyRef
Inherited from
Any
Ungrouped